Clear custom split normal data just for selected faces
You can aim a Data Transfer modifier at a vertex group. Vertices in the group will receive the data from the chosen source. Those not in the group will not.

Top left, below: A cylinder with two regions of faces split out, and left where they were, so the normals do not interpolate. Top right, an intact version of the Cylinder.. ('Form')

.. Bottom left, the 'D_XFer' vertex group. Bottom right, the normals partially transferred from 'Form', to the cylinder with split faces,  according to the group.
If you apply the modifier, its result becomes a Custom Split Normals layer.
So, the steps I was thinking of go as follows:

ShiftD make a duplicate of your problem object
Clear Custom Split Normals on the copy, (giving you some unwanted loss of smoothing, as described)
Assign the vertices whose smoothing you would like to restore from the original to a vertex group.
Give the copy a Data Transfer modifier, targeted on the vertex group, with the original as its source object.

This should pick up the desired normals from the original, leaving the others cleared. When you apply the modifier (in Object Mode), a new Custom Split Normals data layer will be  created on the duplicate, which is a partial copy of the original's. So you will have 'Cleared Custom Split Normal Data for selected faces.'
There may be better approaches altogether, repairing topology by remodelling? or simply reassigning split normals from scratch, using 'Autosmooth' in the object's 'Data' tab 'Normals' panel?... but this is a way to transfer some normals, but not others.